<tool id="bctools_extract_barcodes" name="Extract barcodes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>according to pattern</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        extract_bcs.py
        '$reads'
        #if $barcode_pattern and $barcode_pattern is not None:
            '$barcode_pattern'
        #end if
        --bcs '$extracted_barcodes'
        > '$reads_cleaned'
    ]]></command>
    <inputs>
        <param name="reads" type="data" format="fastq" label="Barcoded sequences" />
        <param name="barcode_pattern" type="text" label="Pattern for extracting barcode nucleotides" help="Starting at 5'-end. X positions will be moved to a separate file, N positions will be kept.">
            <sanitizer invalid_char="N">
                <valid initial="none">
                    <add value="X"/>
                    <add value="N"/>
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="reads_cleaned" format="fastq" label="${tool.name} on ${on_string}: Cleaned reads"/>
        <data name="extracted_barcodes" format="fastq" label="${tool.name} on ${on_string}: Barcodes"/>
    </outputs>
    <tests>
        <test>
            <param name="reads" value="reads.fastq"/>
            <param name="barcode_pattern" value="XXXNNXXX"/>
            <output name="reads_cleaned" file="result_original_head.fastq"/>
            <output name="extracted_barcodes" file="extracted_bcs.fastq"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Extract barcodes according to pattern
===============================================

Exract barcodes from a FASTQ file according to a user-specified pattern and write them to a separate FASTQ file.

    ]]></help>
    <expand macro="citations"/>
</tool>